JAL-3066 Change server to www.compbio.dundee.ac.uk/slivka

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 6f5c18a..5008a3e 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -28,6 +28,7 @@ import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.StringUtils;
+import jalview.workers.InformationThread;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -59,6 +60,10 @@ public class Sequence extends ASequence implements SequenceI
 
   int end;
 
+  HiddenMarkovModel hmm;
+
+  boolean isHMMConsensusSequence = false;
+
   Vector<PDBEntry> pdbIds;
 
   String vamsasId;
@@ -335,6 +340,11 @@ public class Sequence extends ASequence implements SequenceI
         this.addPDBId(new PDBEntry(pdb));
       }
     }
+    if (seq.getHMM() != null)
+    {
+      this.hmm = new HiddenMarkovModel(seq.getHMM(), this);
+    }
+
   }
 
   @Override
@@ -446,18 +456,19 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
-   * DOCUMENT ME!
+   * Answers the sequence name, with '/start-end' appended if jvsuffix is true
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
   @Override
   public String getDisplayId(boolean jvsuffix)
   {
-    StringBuffer result = new StringBuffer(name);
-    if (jvsuffix)
+    if (!jvsuffix)
     {
-      result.append("/" + start + "-" + end);
+      return name;
     }
+    StringBuilder result = new StringBuilder(name);
+    result.append("/").append(start).append("-").append(end);
 
     return result.toString();
   }
@@ -1041,7 +1052,8 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public ContiguousI findPositions(int fromColumn, int toColumn)
   {
-    if (toColumn < fromColumn || fromColumn < 1)
+    fromColumn = Math.max(fromColumn, 1);
+    if (toColumn < fromColumn)
     {
       return null;
     }
@@ -1773,7 +1785,8 @@ public class Sequence extends ASequence implements SequenceI
     {
       for (AlignmentAnnotation ann : annotation)
       {
-        if (ann.calcId != null && ann.calcId.equals(calcId)
+        String id = ann.getCalcId();
+        if (id != null && id.equals(calcId)
                 && ann.label != null && ann.label.equals(label))
         {
           result.add(ann);
@@ -1871,6 +1884,34 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
+  @Override
+  public HiddenMarkovModel getHMM()
+  {
+    return hmm;
+  }
+
+  @Override
+  public void setHMM(HiddenMarkovModel hmm)
+  {
+    this.hmm = hmm;
+  }
+
+  @Override
+  public boolean hasHMMAnnotation()
+  {
+    if (this.annotation == null) {
+      return false;
+    }
+    for (AlignmentAnnotation ann : annotation)
+    {
+      if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
   /**
    * {@inheritDoc}
    */
@@ -2044,4 +2085,10 @@ public class Sequence extends ASequence implements SequenceI
     // otherwise, sequence was completely hidden
     return 0;
   }
+
+  @Override
+  public boolean hasHMMProfile()
+  {
+    return hmm != null;
+  }
 }